createHTOContigList: Generate a contig list from a multiplexed experiment

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Generate a contig list from a multiplexed experiment

Description

This function reprocess and forms a list of contigs for downstream analysis in scRepertoire, createHTOContigList() take the filtered contig annotation output and the single-cell RNA object to create the list. If using an integrated single-cell object, it is recommended to split the object by sequencing run and remove extra prefixes and suffixes on the barcode before using createHTOContigList(). Alternatively, the variable multi.run can be used to separate a list of contigs by a meta data variable. This may have issues with the repeated barcodes.

Usage

createHTOContigList(contig, sc.data, group.by = NULL, multi.run = NULL)

Arguments

contig	The filtered contig annotation file from multiplexed experiment
sc.data	The Seurat or Single-Cell Experiment object.
group.by	One or more meta data headers to create the contig list based on. If more than one header listed, the function combines them into a single variable.
multi.run	If using integrated single-cell object, the meta data variable that indicates the sequencing run.

Value

Returns a list of contigs as input for combineBCR() or combineTCR()

Examples

## Not run: 
filtered.contig <- read.csv(".../Sample/outs/filtered_contig_annotations.csv")

contig.list <- createHTOContigList(contig = filtered.contig, 
                                   sc.data = Seurat.Obj, 
                                   group.by = "HTO_maxID")

## End(Not run)

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.